Somatic Snipper Installation On Mac

Question

[bhaktihd]

Hi

I am trying to install Somatic Sniper on Mac. In the ReadMe file I am not clear with this particular build instruction? Could anyone please clarify what exactly I should be doing here?

h3. Compile SomaticSniper * SomaticSniper does not support in source builds. Create a new build directory, enter it, and run:

bc..         cmake /path/to/somatic-sniper/repo
              make

Also, when I ran the command line below,

h2. Clone the SomaticSniper repository * Recursively clone the git repository

git clone --recursive git://github.com/genome/somatic-sniper.git

I am getting the following error msg: any suggestions on how I can fix this?

user MacBook Pro:somatic-sniper-master User$ git clone --recursive http://github.com/genome/somatic-sniper.git

Cloning into 'somatic-sniper'...
remote: Counting objects: 897, done.
remote: Compressing objects: 100% (413/413), done.
remote: Total 897 (delta 453), reused 857 (delta 413)
Receiving objects: 100% (897/897), 1.43 MiB | 692 KiB/s, done.
Resolving deltas: 100% (453/453), done.
Submodule 'build-common' (git://github.com/genome/build-common.git) registered for path 'build-common'
Cloning into 'build-common'...
fatal: unable to connect to github.com:
github.com[0: 207.97.227.239]: errno=Operation timed out

I would really appreciate any help in regards to installing this program.

Thanks, Bhakti

Answer 1

[Istvan Albert]

The message is pretty obvious - the connection times out - try again later.

Answer 2

[ernfrid]

With regards to your question about in source builds, it simply means that you must create a directory outside the source code to compile the code. Typically, I would do this as so:

1. From your somatic-sniper master branch directory, create a new one called build.
2. From within that directory type cmake ..

or by example:

$ git clone --recursive https://github.com/genome/somatic-sniper.git
$ cd somatic-sniper
$ mkdir build
$ cd build
$ cmake ..
$ make

I'm afraid I have no ideas other than what Istvan has already replied about your timeout issue.